The BioWare Blog has a post from BioWare co-founder Dr. Ray Muzyka confirming that criticism of the ending of Mass Effect 3 has had a massive effect on them, and they will indeed be changing the way the game ends, as they said they might. Here's a bit on their change in plans, and what lead to this point:

Building on their research, Exec Producer Casey Hudson and the team are hard at work on a number of game content initiatives that will help answer the questions, providing more clarity for those seeking further closure to their journey. You’ll hear more on this in April. We’re working hard to maintain the right balance between the artistic integrity of the original story while addressing the fan feedback we’ve received. This is in addition to our existing plan to continue providing new Mass Effect content and new full games, so rest assured that your journey in the Mass Effect universe can, and will, continue.

The reaction to the release of Mass Effect 3 has been unprecedented. On one hand, some of our loyal fans are passionately expressing their displeasure about how their game concluded; we care about this feedback, and we’re planning to directly address it. However, most folks appear to agree that the game as a whole is exceptional, with more than 75 critics giving it a perfect review score and a review average in the mid-90s. Net, I’m proud of the team, but we can and must always strive to do better.

nutshell42 wrote on Mar 21, 2012, 16:23:While the Catalyst didn't appear until 5 min to midnight the existence of a shared consciousness of the Reapers makes a lot of sense.

It's more or less the same arrangement the Geth use now that they've been improved by the Reapers (or used. They either died because you killed them sooner or later or because their Relay blew up) and if you listen to the Reapers in the games they always sound like mixtures between individuality and a hive mind.

Except a specific quote from Sovereign stating that they, the Reapers, are each nations unto themselves...that doesn't support the collected conscience, nor a single unifying controller over them.

The whole arrangement wasn't that bad. There was bound to be a deus ex machina solution because the Reapers were just too powerful. That solution was bound to be a computer virus of some kind because there's no other logical way to kill all the Reapers across the galaxy in a surgical strike.

I expected a MacGuffin somewhere, but in Mass Effect I wasn't expecting a Star Baby to come out of left field in the last five minutes, give me a run-down of the history of the galaxy despite it slapping the established Lore in the face, and then telling me that I am the sole reason that the galaxy must die.

Lo and behold 10 min into Me3 we find the plans for the Crucible which even looks like a virus.

This was the accepted MacGuffin, one that I think everyone expected in some fashion...the writing of the origins of the Crucible is leagues better than what was 'finalized' in the end.

So now we need an attack vector, a way to inject it and what better way than to use the Citadel which we know had a direct connection with the Reapers until the Protheans pulled the plug and which we know could keep up that connection over galactic distances.

But then that leads us back to the Space Baby...if that AI was there the entire time, why did it not step up in ME1 with Sovereign?

I just ignored everything after the part where you have to choose between the Red, Green and Blue Button (did that with Deus Ex, too. It's a surefire sign that the writers have stopped giving a shit and so should you) and was quite happy with the whole thing.

There's a fine line in ignoring and going totally brain-dead...the latter was required to get through the ending unless you wanted to be stuck with a serious kick in the Wolfman Nads..

My main issue is that your war assets have no real meaning at all and the fact that hours of careful galactic diplomacy are worth less than a shitty horde mode with Jim, Bubba and Bill.

The assets have some sway, but thanks to the lack of distinguishing effects in the different endings, it just didn't help portray that fact.